Plasmids are small, circular DNA molecules that are self-replicating and carried by bacteria. They range in size from 2-100kb and can contain genes for antibiotic resistance. Bacterial genomes exist as a single circular chromosome that is highly condensed and packaged. Viruses have RNA or DNA genomes that are either single or double-stranded. Their genomes must be able to be recognized and expressed by their host cell. Mitochondria and chloroplasts originated from endosymbiotic bacteria and contain their own genomes that are maternally inherited and range in size and structure between species. Plant mitochondrial DNA can be much larger than animals.

1. GENOMES OF PLASMID, BACTERIA,
VIRUSES,
ORGANELLES(CHLOROPLAST AND
MITOCHONDRIA)
BY
S. SMITHA
M.Sc – 2ND YEAR
DEPT OF BIOCHEMISTRY AND MOLECULAR
BIOLOGY
PONDICHERRY UNIVERSITY

2. INTRODUCTION
• The genome is the complete set of genes
of an organism.
• Ultimately it is defined by the complete
DNA sequence, although as a practical
matter it may not be possible to identify
every gene unequivocally solely on the
basis of sequence.

3. Plasmid genomes

4. Plasmid genome
• Plasmids are small, double-stranded circular or linear DNA
molecules carried by bacteria, some fungi, and some higher
plants.
• They are extrachromosomal (meaning separate from the host
cell chromosome), independent, and self-replicating.
• At least one copy of a plasmid is passed on to each daughter
cell during cell division.
• Their relationship with their host cell could be considered as
either parasitic or symbiotic.
• They range in size from 2 to 100 kb .
• The majority of plasmids are circular; however, a variety of
linear plasmids have been isolated.

5. •A notable example is the linear plasmid pC1K1 carried by
Claviceps purpurea, a fungus found on rye.
•The fungus contains poisonous alkaloids that cause
ergotism – hallucinations and sometimes death – in
humans who eat the infected grain and was a likely
contributor to the Salem Witch Trials.
• Plasmids are important for our study for two main
reasons: they are carriers of resistance to antibiotics, and
they provide convenient vehicles for recombinant DNA
technology.

6. Schematic representation of a bacterium containing plasmid
DNA.
Plasmids are small, circular molecules of DNA that are
extrachromosomal and self-replicating within the host
bacterium.

7. Bacterial genomes

8. Bacterial genomes
• Prokaryotes do not have a nucleus. However, they still must fit DNA
that is 1000 times the length of the cell within the cell membrane.
• The genome of Escherichia coli, a bacterium widely used in
molecular biology research, is 4700 kb in size and exists as one
double-stranded circular DNA molecule, with no free 5′ or 3′ ends.
• The chromosomal DNA is organized into a condensed ovoid
structure called a nucleoid.
• considerable number of nonessential proteins, called histone-like
proteins or nucleoid-associated proteins, are thought to be involved
in DNA compaction and genome organization.

9. These include HU (heat-unstable protein), IHF (integration host
factor), HNS (heat-stable nucleoid structuring), and SMC (structural
maintenance of chromosomes).
HU and HNS are particularly abundant.
Further condensation packs the bacterial genome into supercoiled
domains of 20–100 kb. Approximately 50% of DNA supercoiling is
unrestrained.
These domains are dynamic and unlikely to have sequence-specific
domain boundaries.
Negative superhelicity is maintained by the action of
topoisomerases, in particular by the ability of gyrase to remove the
positive supercoils generated during replication and transcription.

10. The bacterial genome. Falsecolor
transmission electron micrograph (TEM)
of a lysed bacterial cell (E. coli). The DNA is
visible as the gold colored fibrous mass lying
around the bacterium. Magnification:
×15,700.
(Credit: G. Murti / Photo Researchers, Inc.)

11. GENOMES OF VIRUSES

12. INTRODUCTION ABOUT VIRUS
• Viruses need a living cell to survive
• Viral genome is released inside the
cytoplasm of the host cell
• Virus genomes are made of DNA or RNA
– Not both
– Single stranded (ss) OR double stranded (ds)

13.  Viruses are obligate intracellular parasites:
• genome must contain information which can be
recognized & decoded its host cell
• The viral genetic code must match or at least be
recognized by the host organism.
• Control signals which direct the expression of virus
genes must be appropriate to the host.

14. Viruses And Molecular Biology
• Study of viruses small DNA viruses led to discovery of
promoters for eukaryotic RNA polymerases
• Study of cancer producing viruses led to discovery of
many cellular oncogenes
• RNA splicing in eukaryotic cells was discovered by
studying mRNA from DNA viruses
• Understanding of cellular DNA replication was facilitated
by studying phages and DNA viral replication

15. •The relative simplicity of
virus genomes
(compared with even the
simplest cell) offers a
major advantage - the
ability to 'rescue'
infectious virus from
purified or cloned nucleic
acids.
• Infection of cells caused
by nucleic acid alone is
referred to as
transfection:

16. Viral genome is packaged in protein coat
Nature of Viruses

17. Virus Genomes

18. Types of viral genomes
RNA Viruses
positive stranderd RNA
Negative stranderd RNA
Ambisense (both +ve and –ve )
DNA Viruses
Small DNA Genomes
Large DNA Genomes

19. Positive stranderd RNA Viral genome

20. Negative-Strand RNA Viruses:
Viruses with negative-sense RNA genomes are a little more
diverse than positive-stranded viruses. Possibly because of the
difficulties of expression, they tend to have larger genomes
encoding more genetic information. Because of this,
segmentation is a common though not universal feature of such
viruses.

21. Ambisense Genome Organization:
Some RNA viruses are not strictly 'negative-sense' but ambisense,
since they are part (-)sense & part (+)sense:

22. DNA Virus Genomes
'Small' DNA Genomes:
Bacteriophages have been extensively studied as examples of DNA
virus genomes. Although they vary considerably in size, in general
terms they tend to be relatively small.
As further examples of small DNA genomes,
parvovirus

23. These are very small genomes, & even the
replication-competent parvoviruses contain only
two genes:
 rep, which encodes proteins involved in
transcription &
cap, which encodes the coat proteins.
The ends of the genome have palindromic
sequences of about 115 nt, which form 'hairpins'.
These structures are essential for the initiation of
genome replication.

24. Parvovirus
Parvovirus genomes are:
 linear
 non-segmented
 (+)sense
 single-stranded
DNA
 about 5kb long

25. 'Large' DNA Genomes
• There are a number of virus groups which
have double-stranded DNA genomes of
considerable size & complexity. In many
respects, these viruses are genetically very
similar to the host cells which they infect.
examples of such viruses are the
• adenovirus

26. Adenovirus genomes:
The genomes of adenoviruses consist of linear, double-stranded DNA
of 30-38kbp. These viruses contain 30-40 genes. The terminal
sequences of each DNA strand are inverted repeats of 100-140bp &
therefore, the denatured single strands can form 'panhandle'
structures. These structures are important in DNA replication.

27. Organelle genome

28. Organelle genomes
• Organelles are chloroplast and mitochondria.
Origin of mitochondria and chloroplasts:
 Both mitochondria and chloroplasts are believed to be derived
from endosymbiotic bacteria.
 Endosymbiotic bacteria = free-living prokaryotes that invaded
ancestral eukaryotic cells and established a mutually beneficial
relationship.
 Many required mitochondria and chloroplast proteins also are
coded by nuclear genes.
 numt = nuclear mtDNA (mtDNA transposed to the nucleus)

29. Mitochondrial genome

30. Mitochondrial genome
• Mitochondrial genomes are extremey diverse
having charecteristic difference in size and
structural organisation.
• Randomly encodes for gene expression
function.
• All three classes for self-splicing introns.
• tRNA genes in functional clusters while rRNA
dispersed.

31. Mitochondrial molecular genetics
• inheritance of mitochondria
- petite mutants of yeast
• biogenesis of mitochondria by fission

32. Plant mitochondrial DNA
• chromosome size is much bigger but varies dramatically between
species (200-2000 kb)
• arranged as different size circles, sometimes with plasmids.
• The plant mtDNA contains chloroplast sequences, indicating
exchange of genetic information between organelles in plants.
• Much of the plant mtDNA is non-coding, but coding regions are larger
than animals and fungi.
• Number of proteins synthesised not known definitely but more than in
animals and yeast (probably about 50)
Plant mitochondria have specialised functions
• in leaves they participate in photorespiration
• sites of vitamin synthesis (vit C, folic acid, biotin)

33. Yeast mitochondrial genome
• Yeast mtDNA
• 68-75 kb, similar in structure to bacterial
genome
• contains introns and non-regions between
genes.
• Same proteins made as in animals
• genes transcribed separately

34. Yeast
mitochondrial
chromosome

35. Human mtDNA
• small, double stranded
circular chromosome
• 16,569 bp in total
• no non-coding DNA
• no introns
• polycistronic replication
which is initiated from
the D (displacement)-
loop region
• followed by splicing of
transcript to form
messages.
Organisation of the mitochondrial
chromosome

36. Mitochondrial Inheritance
Yeast has been used extensively to study
mitochondrial inheritance.
There is a Yeast strain, called "Petite" that have
structurally abnormal mitochondria that are incapable
of oxidative phosphorylation. These mitochondria
have lost some or all of their DNA.
Genetic crosses between petite and wt strains
showed that inheritance of this trait did not segregate
with any of the nuclear chromosomes.

37. Mitochondrial Inheritance in Yeast

38. This led to the suggestion that some genetic
element existed in the cytoplasm and was
inherited in a different manner from nuclear
genes. This is called “non-Mendelian
inheritance” or “cytoplasmic inheritance”.
In yeast and animals, this indicated inheritance of
mitochondrial genes: in plants it also includes
inheritance of chloroplast genes

39. plastids
• Genomes are circular-ranges between
110&150 bp
• Encodes protein & structural RNAs
required for chloroplast gene expression
tRNA, rRNA
• Encodes proteins with direct function in
photosynthesis
• Chloroplast genomes may be unique
sequences seperated by inverted repeats.